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Extending solomon output masks
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Hello CCP4 users -
I am in the throes of determining an NCS operation for my dimeric protein. Towards this end, I am trying to manually
edit a solvent mask generated from SOLOMON to envelope what I believe is the dimer. As things stand, crystallographic
contacts are obfuscating the true shape of the dimer - it is these contacts which I am trying to edit out of the mask.
I used the the SLVMASK option in SOLOMON to output a mask. I am now trying to use MAPMASK to extend this slightly
beyond my assymetric unit so that I can see the entire dimer. However, SOLOMON and MAPMASK don't seem to get along to
well, as evidenced by this error message:
Data line--- xyzlim 0 100 -15 82 -30 50
Data line--- EXTEND XTAL OVERLAP
Data line--- END
(Q)QOPEN allocated # 1
User: byron Logical Name: MSKIN1
Status: READONLY Filename: recent_solomon.mask
File name for input map file on unit 1 : recent_solomon.mask
file size = 212224 ; logical name MSKIN1
Number of columns, rows, sections ............... 33 80 80
Map mode ........................................ 0
Start and stop points on columns, rows, sections 0 32 0 79 0 79
Grid sampling on x, y, z ........................ 80 80 256
Cell dimensions ................................. 80.97 80.97 249.67 90.00 90.00 90.00
Fast, medium, slow axes ......................... Z X Y
Space-group ..................................... 1
Number of titles ................................ 1
.....
(Q)QOPEN allocated # 1
User: byron Logical Name: MSKIN1
Status: READONLY Filename: recent_solomon.mask
MAP/MASK READ SUCCESSFUL
mapmask: mapoverlap - map does not contain a whole ASU
mapmask: mapoverlap - map does not contain a whole ASU
As a quick reminder, the ASU for P43212 is 0<x<1 0<y<1 0<z<1/8th (so x=80 y=80 z=31.2 A should contain an ASU for my
cell of 80 80 249.67)
The problem seems to be rounding errors with regards to the Z axis, as this is the only grid spacing less than 1
angstrom. X and Y axes behave alright and can be extended properly if I use the PAD command in MAPMASK, but I can't see
anything beyond the assymetric unit along the Z direction. Is this a quirk/bug in either SOLOMON or MAPMASK, or am I
(once again) making a foolish mistake?
Thanks in advance for help rendered!
--
Byron Delabarre "In reciprocal space, I'm a somebody"
Department of Biochemistry
McMaster University
Hamilton, Ontario, CANADA Phone: 905 525 9140 x22428